Variant report

Variant	rs3789068
Chromosome Location	chr2:111909247-111909248
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:111904094..111906094-chr2:111907490..111909411,2	K562	blood:
2	chr2:111877254..111880107-chr2:111907891..111910669,3	MCF-7	breast:
3	chr2:111898288..111899933-chr2:111909236..111912123,2	MCF-7	breast:
4	chr2:111908889..111912650-chr2:111913832..111916380,3	MCF-7	breast:
5	chr2:111877614..111879979-chr2:111908641..111910438,3	K562	blood:
6	chr2:111877202..111881841-chr2:111904437..111911865,11	K562	blood:

Variant related genes	Relation type
ENSG00000153094	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10166773	0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs10169613	0.83[ASN][1000 genomes]
rs10189015	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10211562	0.80[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs10439396	0.83[ASN][1000 genomes]
rs1054873	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11674517	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11899831	0.80[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs13398360	0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs1439287	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1821968	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1837366	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1837367	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1837368	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1837369	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2165107	0.80[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2241841	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2241842	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2241844	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28723045	0.83[ASN][1000 genomes]
rs3789061	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3789064	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3789065	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4302219	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4627572	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4848406	0.84[ASN][1000 genomes]
rs4849402	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4849403	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55878194	0.83[ASN][1000 genomes]
rs56952027	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60286362	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60982612	0.83[ASN][1000 genomes]
rs616130	0.83[TSI][hapmap]
rs6542350	0.82[ASN][1000 genomes]
rs6708784	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6726007	0.86[CEU][hapmap];0.83[CHB][hapmap];0.89[JPT][hapmap];0.80[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6732491	0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs6734942	0.98[ASN][1000 genomes]
rs6760053	0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs7565473	0.82[ASN][1000 genomes]
rs7567184	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs7569300	0.81[ASN][1000 genomes]
rs7572367	0.82[ASN][1000 genomes]
rs7577824	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7581735	0.83[ASN][1000 genomes]
rs7585054	0.81[ASN][1000 genomes]
rs7588534	0.81[ASN][1000 genomes]
rs7593638	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7596789	0.80[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs7602904	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9308731	0.83[CHB][hapmap]
rs9308742	0.82[ASN][1000 genomes]
rs9808225	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874838	chr2:111376870-112046226	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv834331	chr2:111812139-112004678	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	esv1803356	chr2:111899783-112662597	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv428402	chr2:111899783-112662597	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
5	esv1801950	chr2:111899783-112746937	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
6	esv2757825	chr2:111899783-112746937	Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
7	esv2759083	chr2:111899783-112746937	Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3789068	BCL2L11	cis	cerebellum	SCAN
rs3789068	SULT1C2	cis	cerebellum	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:111881200-111909600	Weak transcription	NHLF	lung
2	chr2:111881200-111912800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr2:111881800-111909600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr2:111881800-111919800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr2:111883400-111909400	Weak transcription	Aorta	Aorta
6	chr2:111883400-111912600	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr2:111883600-111909400	Weak transcription	Brain Cingulate Gyrus	brain
8	chr2:111883600-111909600	Weak transcription	Small Intestine	intestine
9	chr2:111884600-111909400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr2:111884800-111925400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr2:111887400-111912000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr2:111890600-111914400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr2:111893600-111913400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr2:111893600-111916800	Weak transcription	HSMM	muscle
15	chr2:111893600-111918600	Weak transcription	Colon Smooth Muscle	Colon
16	chr2:111894200-111917200	Weak transcription	NH-A	brain
17	chr2:111894400-111909600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr2:111895000-111912800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr2:111895400-111909600	Weak transcription	Brain Hippocampus Middle	brain
20	chr2:111897600-111912800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr2:111897600-111913000	Weak transcription	Stomach Mucosa	stomach
22	chr2:111897800-111909600	Weak transcription	Pancreas	Pancrea
23	chr2:111897800-111910000	Weak transcription	Stomach Smooth Muscle	stomach
24	chr2:111897800-111910600	Strong transcription	HepG2	liver
25	chr2:111897800-111912400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr2:111897800-111912600	Weak transcription	Brain Anterior Caudate	brain
27	chr2:111897800-111916600	Weak transcription	Psoas Muscle	Psoas
28	chr2:111898000-111911400	Strong transcription	Liver	Liver
29	chr2:111898200-111909400	Weak transcription	Fetal Muscle Leg	muscle
30	chr2:111898200-111912600	Weak transcription	NHEK	skin
31	chr2:111898800-111909400	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr2:111898800-111909600	Weak transcription	Lung	lung
33	chr2:111898800-111912400	Weak transcription	HMEC	breast
34	chr2:111898800-111912800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr2:111898800-111920600	Weak transcription	Fetal Kidney	kidney
36	chr2:111899800-111909600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr2:111902400-111909400	Weak transcription	HSMMtube	muscle
38	chr2:111902800-111912400	Weak transcription	Hela-S3	cervix
39	chr2:111902800-111915200	Weak transcription	Fetal Brain Female	brain
40	chr2:111904400-111920800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr2:111904800-111912800	Strong transcription	Fetal Thymus	thymus
42	chr2:111905600-111915200	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr2:111906000-111915800	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr2:111906200-111909400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr2:111906400-111909800	Weak transcription	Left Ventricle	heart
46	chr2:111906400-111912200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr2:111906400-111914000	Strong transcription	Dnd41	blood
48	chr2:111906400-111919600	Strong transcription	HUES48 Cell Line	embryonic stem cell
49	chr2:111906600-111914200	Weak transcription	GM12878-XiMat	blood
50	chr2:111906600-111927000	Weak transcription	Rectal Smooth Muscle	rectum

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